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1.55 Angstrom Resolution Crystal Structure of Peptidase T (pepT-1) from Bacillus anthracis str. 'Ames Ancestor'.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FNO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 Protein solution: 7.5mg/mL, 0.25M NaCl, Tris-HCl pH(8.3);
Screen solution: JCSG+, E2, 0.2M NaCl, 2M Ammonium sulfate, 0.1M Na-Cacodilate pH(6.5) VAPOR DIFFUSION, SITTING DROP, temperature 295K; Cryo: 25% Sucrose, 1.8M Ammonium sulfate.
Crystal Properties Matthews coefficient Solvent content 2.68 54.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.216 α = 90 b = 142.739 β = 90 c = 40.993 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD Beryllium lenses 2009-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.55 30 99.9 0.068 25.8 7.3 77209 77209 -3 21
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 99.3 0.554 3.3 6.5 3814
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1fno 1.55 29.11 73110 73110 3863 99.94 0.14954 0.14954 0.14836 0.1832 0.17173 0.203 RANDOM 12.404
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.09 -0.36 1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.925 r_dihedral_angle_4_deg 13.661 r_dihedral_angle_3_deg 9.079 r_scangle_it 4.329 r_dihedral_angle_1_deg 3.19 r_scbond_it 2.664 r_angle_refined_deg 1.493 r_mcangle_it 1.481 r_angle_other_deg 0.879 r_mcbond_it 0.854
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.925 r_dihedral_angle_4_deg 13.661 r_dihedral_angle_3_deg 9.079 r_scangle_it 4.329 r_dihedral_angle_1_deg 3.19 r_scbond_it 2.664 r_angle_refined_deg 1.493 r_mcangle_it 1.481 r_angle_other_deg 0.879 r_mcbond_it 0.854 r_mcbond_other 0.288 r_chiral_restr 0.098 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3282 Nucleic Acid Atoms Solvent Atoms 586 Heterogen Atoms 59
Software Software Software Name Purpose Blu-Ice data collection CRANK phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling